Feature wish: --indep-r2

[kforner]

Hi,
It would be nice to have a --indep-r2, (or --indep-pairwise dprime) that selects tag SNPs based on the real (haplotype-based) r^2.
Rationale:

• the non-haplotype based r^2 is an approximation
• it seems that the haplotype-based r^2 is slower to compute, but not that slow. On my tests it is roughly 3 times slower to compute
• it would be consistent with --ld

Anyway, thanks for this great software.

[chrchang]

A fully powered version of this (capable of using SHAPEIT's results, etc.) is planned for PLINK 2.0. I'll ask around and see if there's substantial demand for a "bad phasing" --indep-pairwise in v1.9, though.

[kforner]

When you say "bad phasing", you mean a pairwise maximum-likelihood estimate of the phase as opposed to the shapeit algorithm that uses information from all snps I guess ?

[chrchang]

Correct. There's existing software which performs the more accurate r^2 computation (e.g. VCFtools --hap-r2), and one can write a script to select variants in an indep-pairwise-like manner using those results if the additional accuracy is important today.

[kforner]

I just saw that you recommend to use the google group for feedback. Do you prefer that I post the feature request there for the record ?

[chrchang]

That's a good way to gauge additional interest in this feature, yes.

[kforner]

moved to https://groups.google.com/forum/#!forum/plink2-users